This is probably Timothy Zahn's Manta's Gift.
From the Goodreads summary:
When Matt Raimey had his accident, he thought his life was over. He never dreamed, in his wildest fantasies, that he'd end up in a spot like this. In the toxic atmosphere of Jupiter, born into the body of an enormous creature that looked like a cross between a manta ray and a dolphin, he is living a new life, unlike any humankind had previously experienced.
Also at the Science Fiction Review with more details about the story (although without revealing the ending).
When I searched Google for
science fiction manta rays jupiter, the top hits were all about this book. Then again, Google search results are different for everyone, and I've done a lot of searching for science fiction stories to answer people's story-ID questions; maybe you'd get completely different results with the same search.
Iain M Banks, The Algebraist. It involves nearly immortal manta ray like creatures living in a gas giant, with a gate in its core.